Dysbiosis of the Gut Microbiome is associated with Tumor Biomarkers in Lung Cancer

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/11

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

31595156

DOI Digital object identifier for electronic documents.

10.7150/ijbs.35980

URI

Authors

Liu F, Li J, Guan Y, Lou Y, Chen H, Xu M, Deng D, Chen J, Ni B, Zhao L, Li H, Sang H, Cai X

Journal

International journal of biological sciences

Year

2019

Keywords:

16SrRNAsequencing, Carcinoembryonic antigen, Cytokeratin 19 fragment, Fecal, Gut microbiome, Lung cancer, Neuron specific enolase

Lung cancer is a malignancy with high morbidity and mortality worldwide. More evidences indicated that gut microbiome plays an important role in the carcinogenesis and progression of cancers by metabolism, inflammation and immune response. However, the study about the characterizations of gut microbiome in lung cancer is limited. In this study, the fecal samples were collected from 16 healthy individuals and 30 lung cancer patients who were divided into 3 groups based on different tumor biomarkers (cytokeratin 19 fragment, neuron specific enolase and carcinoembryonic antigen, respectively) and were analyzed using 16S rRNA gene amplicon sequencing. Each lung cancer group has characterized gut microbial community and presents an elimination, low-density, and loss of bacterial diversity microbial ecosystem compared to that of the healthy control. The microbiome structures in family and genera levels are more complex and significantly varied from each group presenting more different and special pathogen microbiome such as Enterobacteriaceae, Streptococcus, Prevotella, etc and fewer probiotic genera including Blautia, Coprococcus, Bifidobacterium and Lachnospiraceae. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and COG annotation demonstrated decreased abundance of some dominant metabolism-related pathways in the lung cancer. This study explores for the first time the features of gut microbiome in lung cancer patients and may provide new insight into the pathogenesis of lung cancer system, with the implication that gut microbiota may serve as a microbial marker and contribute to the derived metabolites, development and differentiation in lung cancer system.

Experiment 1

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Subjects

Location of subjects: China

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Lung carcinoma

Group 0 name Corresponds to the control (unexposed) group for case-control studies: healthy control

Group 1 name Corresponds to the case (exposed) group for case-control studies: lung cancer group

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: newly diagnosed lung cancer patients by histopathology and computed tomography

Group 0 sample size Number of subjects in the control (unexposed) group: 16

Group 1 sample size Number of subjects in the case (exposed) group: 30

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 1 month

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased

Chao1 Abundance-based estimator of species richness: unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness: decreased

Richness Number of species: unchanged

Signature 1

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Curated date: 2021/01/10

Curator: Fatima Zohra

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Source: Figure 3B

Description: Comparison of relative abundant microbiome at family level between cancer groups and healthy controls

Abundance in Group 1: decreased abundance in

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Lachnospiraceae

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Experiment 2

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: controls + other lung cancer groups

Group 1 name Corresponds to the case (exposed) group for case-control studies: CEA group

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: newly diagnosed lung cancer patients who are CEA-positive

Group 0 sample size Number of subjects in the control (unexposed) group: 35

Group 1 sample size Number of subjects in the case (exposed) group: 11

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased

Chao1 Abundance-based estimator of species richness: unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness: decreased

Richness Number of species: unchanged

Signature 1

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Curator: Fatima Zohra

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Source: Figure 3B

Description: Comparison of relatively abundant microbiota between CEA group and other study groups

Abundance in Group 1: increased abundance in CEA group

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Bacteroidaceae
Streptococcaceae

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Experiment 3

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Curated date: 2021/01/10

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Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: NSE group

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: newly diagnosed lung cancer patients who are NSE positive

Group 0 sample size Number of subjects in the control (unexposed) group: 37

Group 1 sample size Number of subjects in the case (exposed) group: 9

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased

Chao1 Abundance-based estimator of species richness: unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness: decreased

Richness Number of species: unchanged

Signature 1

Edit History Delete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 3B

Description: Differentially abundant microbiota between NSE group and the other study groups

Abundance in Group 1: increased abundance in NSE group

NCBI	Quality Control	Links
Enterobacteriaceae
Fusobacteriaceae
Verrucomicrobiaceae

Revision editor(s): Claregrieve1, WikiWorks

Experiment 4

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Curated date: 2021/01/10

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: healthy controls

Group 1 name Corresponds to the case (exposed) group for case-control studies: CYF group

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: newly diagnosed lung cancer patients who are CYFRA positive